[?2004h(base) gskoksharova@genedev2:~$ cd /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM [?2004l [?2004h(base) gskoksharova@genedev2:/sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM$ f astqc [?2004l Command 'fastqc' not found, but can be installed with: apt install fastqc Please ask your administrator. [?2004h(base) gskoksharova@genedev2:/sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM$ conda install bioconda::fastqc [?2004l Retrieving notices: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done Channels: - conda-forge - bioconda - defaults Platform: linux-64 Collecting package metadata (repodata.json): - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done Solving environment: - \ | / done ## Package Plan ## environment location: /home/gskoksharova/miniconda3 added / updated specs: - bioconda::fastqc The following packages will be downloaded: package | build ---------------------------|----------------- alsa-lib-1.2.6.1 | h7f98852_0 578 KB conda-forge bedtools-2.31.1 | h13024bc_3 1.5 MB bioconda ca-certificates-2026.1.4 | hbd8a1cb_0 143 KB conda-forge cairo-1.16.0 | hb05425b_5 1.2 MB certifi-2026.1.4 | pyhd8ed1ab_0 147 KB conda-forge conda-24.11.3 | py312h7900ff3_0 1.1 MB conda-forge fastqc-0.12.1 | hdfd78af_0 11.1 MB bioconda font-ttf-dejavu-sans-mono-2.37| hab24e00_0 388 KB conda-forge font-ttf-inconsolata-3.000 | h77eed37_0 94 KB conda-forge font-ttf-source-code-pro-2.038| h77eed37_0 684 KB conda-forge font-ttf-ubuntu-0.83 | h77eed37_3 1.5 MB conda-forge fontconfig-2.14.1 | h55d465d_3 281 KB fonts-conda-ecosystem-1 | 0 4 KB conda-forge fonts-conda-forge-1 | hc364b38_1 4 KB conda-forge freetype-2.14.1 | ha770c72_0 169 KB conda-forge gettext-0.25.1 | h3f43e3d_1 529 KB conda-forge gettext-tools-0.25.1 | h3f43e3d_1 3.5 MB conda-forge giflib-5.2.2 | hd590300_0 75 KB conda-forge glib-2.72.1 | h6239696_0 443 KB conda-forge glib-tools-2.72.1 | h6239696_0 107 KB conda-forge graphite2-1.3.14 | hecca717_2 97 KB conda-forge harfbuzz-4.3.0 | hf52aaf7_2 1.3 MB jpeg-9e | h0b41bf4_3 235 KB conda-forge lcms2-2.15 | hfd0df8a_0 235 KB conda-forge lerc-4.0.0 | h0aef613_1 258 KB conda-forge libarchive-3.7.7 | h75ea233_4 846 KB conda-forge libasprintf-0.25.1 | h3f43e3d_1 52 KB conda-forge libasprintf-devel-0.25.1 | h3f43e3d_1 34 KB conda-forge libcups-2.3.3 | h36d4200_3 4.3 MB conda-forge libcurl-8.1.2 | h409715c_0 364 KB conda-forge libdeflate-1.17 | h0b41bf4_0 63 KB conda-forge libfreetype-2.14.1 | ha770c72_0 7 KB conda-forge libfreetype6-2.14.1 | h73754d4_0 378 KB conda-forge libgcc-15.2.0 | he0feb66_16 1018 KB conda-forge libgcc-ng-15.2.0 | h69a702a_16 27 KB conda-forge libgettextpo-0.25.1 | h3f43e3d_1 184 KB conda-forge libgettextpo-devel-0.25.1 | h3f43e3d_1 37 KB conda-forge libglib-2.72.1 | h2d90d5f_0 3.1 MB conda-forge libgomp-15.2.0 | he0feb66_16 589 KB conda-forge libiconv-1.18 | h3b78370_2 772 KB conda-forge liblzma-5.8.2 | hb03c661_0 111 KB conda-forge liblzma-devel-5.8.2 | hb03c661_0 454 KB conda-forge libmamba-1.5.11 | hfe524e5_1 1.9 MB libmambapy-1.5.11 | py312haf1ee3a_1 340 KB libnghttp2-1.52.0 | h61bc06f_0 608 KB conda-forge libpng-1.6.54 | h421ea60_0 310 KB conda-forge libsolv-0.7.35 | h9463b59_0 506 KB conda-forge libstdcxx-15.2.0 | h934c35e_16 5.6 MB conda-forge libstdcxx-ng-15.2.0 | hdf11a46_16 27 KB conda-forge libtiff-4.5.0 | h6adf6a1_2 397 KB conda-forge libwebp-base-1.6.0 | hd42ef1d_0 419 KB conda-forge libxcb-1.17.0 | h8a09558_0 387 KB conda-forge libxcrypt-4.4.36 | hd590300_1 98 KB conda-forge libxml2-2.13.9 | h2c43086_0 669 KB lz4-c-1.10.0 | h5888daf_1 163 KB conda-forge lzo-2.10 | h280c20c_1002 187 KB conda-forge openjdk-11.0.15 | hc6918da_0 174.0 MB conda-forge openssl-3.6.1 | h35e630c_1 3.0 MB conda-forge pcre-8.45 | h9c3ff4c_0 253 KB conda-forge pcre2-10.47 | haa7fec5_0 1.2 MB conda-forge perl-5.32.1 | 7_hd590300_perl5 12.7 MB conda-forge pixman-0.46.4 | h54a6638_1 440 KB conda-forge pthread-stubs-0.4 | hb9d3cd8_1002 8 KB conda-forge python-3.12.9 | h5148396_0 34.7 MB python_abi-3.12 | 3_cp312 6 KB seqkit-2.12.0 | he881be0_1 6.5 MB bioconda sqlite-3.50.2 | hb25bd0a_1 1.1 MB tk-8.6.15 | h54e0aa7_0 3.4 MB xorg-libx11-1.8.12 | h4f16b4b_0 816 KB conda-forge xorg-libxau-1.0.12 | hb03c661_1 15 KB conda-forge xorg-libxdmcp-1.1.5 | hb03c661_1 20 KB conda-forge xorg-libxext-1.3.7 | hb03c661_0 49 KB conda-forge xorg-libxfixes-6.0.2 | hb03c661_0 20 KB conda-forge xorg-libxi-1.8.2 | hb9d3cd8_0 46 KB conda-forge xorg-libxrender-0.9.12 | hb9d3cd8_0 32 KB conda-forge xorg-libxtst-1.2.5 | hb9d3cd8_3 32 KB conda-forge xz-5.8.2 | ha02ee65_0 24 KB conda-forge xz-gpl-tools-5.8.2 | ha02ee65_0 33 KB conda-forge xz-tools-5.8.2 | hb03c661_0 94 KB conda-forge zlib-1.3.1 | hb9d3cd8_2 90 KB conda-forge zstandard-0.25.0 | py312h5253ce2_1 456 KB conda-forge zstd-1.5.7 | hb78ec9c_6 587 KB conda-forge ------------------------------------------------------------ Total: 288.9 MB The following NEW packages will be INSTALLED: alsa-lib conda-forge/linux-64::alsa-lib-1.2.6.1-h7f98852_0 cairo pkgs/main/linux-64::cairo-1.16.0-hb05425b_5 fastqc bioconda/noarch::fastqc-0.12.1-hdfd78af_0 font-ttf-dejavu-s~ conda-forge/noarch::font-ttf-dejavu-sans-mono-2.37-hab24e00_0 font-ttf-inconsol~ conda-forge/noarch::font-ttf-inconsolata-3.000-h77eed37_0 font-ttf-source-c~ conda-forge/noarch::font-ttf-source-code-pro-2.038-h77eed37_0 font-ttf-ubuntu conda-forge/noarch::font-ttf-ubuntu-0.83-h77eed37_3 fontconfig pkgs/main/linux-64::fontconfig-2.14.1-h55d465d_3 fonts-conda-ecosy~ conda-forge/noarch::fonts-conda-ecosystem-1-0 fonts-conda-forge conda-forge/noarch::fonts-conda-forge-1-hc364b38_1 freetype conda-forge/linux-64::freetype-2.14.1-ha770c72_0 gettext conda-forge/linux-64::gettext-0.25.1-h3f43e3d_1 gettext-tools conda-forge/linux-64::gettext-tools-0.25.1-h3f43e3d_1 giflib conda-forge/linux-64::giflib-5.2.2-hd590300_0 glib conda-forge/linux-64::glib-2.72.1-h6239696_0 glib-tools conda-forge/linux-64::glib-tools-2.72.1-h6239696_0 graphite2 conda-forge/linux-64::graphite2-1.3.14-hecca717_2 harfbuzz pkgs/main/linux-64::harfbuzz-4.3.0-hf52aaf7_2 jpeg conda-forge/linux-64::jpeg-9e-h0b41bf4_3 lcms2 conda-forge/linux-64::lcms2-2.15-hfd0df8a_0 lerc conda-forge/linux-64::lerc-4.0.0-h0aef613_1 libasprintf conda-forge/linux-64::libasprintf-0.25.1-h3f43e3d_1 libasprintf-devel conda-forge/linux-64::libasprintf-devel-0.25.1-h3f43e3d_1 libcups conda-forge/linux-64::libcups-2.3.3-h36d4200_3 libdeflate conda-forge/linux-64::libdeflate-1.17-h0b41bf4_0 libfreetype conda-forge/linux-64::libfreetype-2.14.1-ha770c72_0 libfreetype6 conda-forge/linux-64::libfreetype6-2.14.1-h73754d4_0 libgcc conda-forge/linux-64::libgcc-15.2.0-he0feb66_16 libgettextpo conda-forge/linux-64::libgettextpo-0.25.1-h3f43e3d_1 libgettextpo-devel conda-forge/linux-64::libgettextpo-devel-0.25.1-h3f43e3d_1 libglib conda-forge/linux-64::libglib-2.72.1-h2d90d5f_0 libiconv conda-forge/linux-64::libiconv-1.18-h3b78370_2 liblzma conda-forge/linux-64::liblzma-5.8.2-hb03c661_0 liblzma-devel conda-forge/linux-64::liblzma-devel-5.8.2-hb03c661_0 libpng conda-forge/linux-64::libpng-1.6.54-h421ea60_0 libstdcxx conda-forge/linux-64::libstdcxx-15.2.0-h934c35e_16 libtiff conda-forge/linux-64::libtiff-4.5.0-h6adf6a1_2 libwebp-base conda-forge/linux-64::libwebp-base-1.6.0-hd42ef1d_0 libxcb conda-forge/linux-64::libxcb-1.17.0-h8a09558_0 libxcrypt conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1 libzlib conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2 lzo conda-forge/linux-64::lzo-2.10-h280c20c_1002 openjdk conda-forge/linux-64::openjdk-11.0.15-hc6918da_0 pcre conda-forge/linux-64::pcre-8.45-h9c3ff4c_0 perl conda-forge/linux-64::perl-5.32.1-7_hd590300_perl5 pixman conda-forge/linux-64::pixman-0.46.4-h54a6638_1 pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-hb9d3cd8_1002 python_abi pkgs/main/linux-64::python_abi-3.12-3_cp312 xorg-libx11 conda-forge/linux-64::xorg-libx11-1.8.12-h4f16b4b_0 xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.12-hb03c661_1 xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.5-hb03c661_1 xorg-libxext conda-forge/linux-64::xorg-libxext-1.3.7-hb03c661_0 xorg-libxfixes conda-forge/linux-64::xorg-libxfixes-6.0.2-hb03c661_0 xorg-libxi conda-forge/linux-64::xorg-libxi-1.8.2-hb9d3cd8_0 xorg-libxrender conda-forge/linux-64::xorg-libxrender-0.9.12-hb9d3cd8_0 xorg-libxtst conda-forge/linux-64::xorg-libxtst-1.2.5-hb9d3cd8_3 xz-gpl-tools conda-forge/linux-64::xz-gpl-tools-5.8.2-ha02ee65_0 xz-tools conda-forge/linux-64::xz-tools-5.8.2-hb03c661_0 The following packages will be UPDATED: bedtools 2.27.1-h9a82719_5 --> 2.31.1-h13024bc_3 ca-certificates pkgs/main/linux-64::ca-certificates-2~ --> conda-forge/noarch::ca-certificates-2026.1.4-hbd8a1cb_0 certifi pkgs/main/linux-64::certifi-2025.8.3-~ --> conda-forge/noarch::certifi-2026.1.4-pyhd8ed1ab_0 conda pkgs/main::conda-24.11.1-py312h06a430~ --> conda-forge::conda-24.11.3-py312h7900ff3_0 libarchive pkgs/main::libarchive-3.7.4-hfab0078_0 --> conda-forge::libarchive-3.7.7-h75ea233_4 libgcc-ng pkgs/main::libgcc-ng-11.2.0-h1234567_1 --> conda-forge::libgcc-ng-15.2.0-h69a702a_16 libgomp pkgs/main::libgomp-11.2.0-h1234567_1 --> conda-forge::libgomp-15.2.0-he0feb66_16 libmamba 1.5.11-hfe524e5_0 --> 1.5.11-hfe524e5_1 libmambapy 1.5.11-py312haf1ee3a_0 --> 1.5.11-py312haf1ee3a_1 libsolv pkgs/main::libsolv-0.7.24-he621ea3_1 --> conda-forge::libsolv-0.7.35-h9463b59_0 libstdcxx-ng pkgs/main::libstdcxx-ng-11.2.0-h12345~ --> conda-forge::libstdcxx-ng-15.2.0-hdf11a46_16 libxml2 2.13.5-hfdd30dd_0 --> 2.13.9-h2c43086_0 lz4-c pkgs/main::lz4-c-1.9.4-h6a678d5_1 --> conda-forge::lz4-c-1.10.0-h5888daf_1 openssl pkgs/main::openssl-3.0.17-h5eee18b_0 --> conda-forge::openssl-3.6.1-h35e630c_1 pcre2 pkgs/main::pcre2-10.42-hebb0a14_1 --> conda-forge::pcre2-10.47-haa7fec5_0 python 3.12.8-h5148396_0 --> 3.12.9-h5148396_0 seqkit 2.10.1-he881be0_0 --> 2.12.0-he881be0_1 sqlite 3.45.3-h5eee18b_0 --> 3.50.2-hb25bd0a_1 tk 8.6.14-h39e8969_0 --> 8.6.15-h54e0aa7_0 xz pkgs/main::xz-5.4.6-h5eee18b_1 --> conda-forge::xz-5.8.2-ha02ee65_0 zlib pkgs/main::zlib-1.2.13-h5eee18b_1 --> conda-forge::zlib-1.3.1-hb9d3cd8_2 zstandard pkgs/main::zstandard-0.23.0-py312h2c3~ --> conda-forge::zstandard-0.25.0-py312h5253ce2_1 zstd pkgs/main::zstd-1.5.6-hc292b87_0 --> conda-forge::zstd-1.5.7-hb78ec9c_6 The following packages will be SUPERSEDED by a higher-priority channel: libcurl pkgs/main::libcurl-8.9.1-h251f7ec_0 --> conda-forge::libcurl-8.1.2-h409715c_0 libnghttp2 pkgs/main::libnghttp2-1.57.0-h2d74bed~ --> conda-forge::libnghttp2-1.52.0-h61bc06f_0 libssh2 pkgs/main::libssh2-1.11.1-h251f7ec_0 --> conda-forge::libssh2-1.11.1-hcf80075_0 Proceed ([y]/n)? y Downloading and Extracting Packages: openjdk-11.0.15 | 174.0 MB | | 0% python-3.12.9 | 34.7 MB | | 0%  perl-5.32.1 | 12.7 MB | | 0%  fastqc-0.12.1 | 11.1 MB | | 0%  seqkit-2.12.0 | 6.5 MB | | 0%  libstdcxx-15.2.0 | 5.6 MB | | 0%  libcups-2.3.3 | 4.3 MB | | 0%  gettext-tools-0.25.1 | 3.5 MB | | 0%  tk-8.6.15 | 3.4 MB | | 0%  libglib-2.72.1 | 3.1 MB | | 0%  openssl-3.6.1 | 3.0 MB | | 0%  libmamba-1.5.11 | 1.9 MB | | 0%  font-ttf-ubuntu-0.83 | 1.5 MB | | 0%  bedtools-2.31.1 | 1.5 MB | | 0%  harfbuzz-4.3.0 | 1.3 MB | | 0%  pcre2-10.47 | 1.2 MB | | 0%  cairo-1.16.0 | 1.2 MB | | 0%  conda-24.11.3 | 1.1 MB | | 0%  sqlite-3.50.2 | 1.1 MB | | 0%  libgcc-15.2.0 | 1018 KB | | 0%  libarchive-3.7.7 | 846 KB | | 0%  xorg-libx11-1.8.12 | 816 KB | | 0%  libiconv-1.18 | 772 KB | | 0%  ... (more hidden) ... perl-5.32.1 | 12.7 MB | 1 | 0%  fastqc-0.12.1 | 11.1 MB | 1 | 0%  seqkit-2.12.0 | 6.5 MB | 2 | 0%  openjdk-11.0.15 | 174.0 MB | | 0% perl-5.32.1 | 12.7 MB | # | 1%  python-3.12.9 | 34.7 MB | | 0%  fastqc-0.12.1 | 11.1 MB | #6 | 2%  seqkit-2.12.0 | 6.5 MB | ### | 3%  openjdk-11.0.15 | 174.0 MB | 1 | 0% perl-5.32.1 | 12.7 MB | #####9 | 6%  python-3.12.9 | 34.7 MB | 3 | 0%  fastqc-0.12.1 | 11.1 MB | ###5 | 3%  openjdk-11.0.15 | 174.0 MB | 2 | 0% seqkit-2.12.0 | 6.5 MB | ##### | 5%  perl-5.32.1 | 12.7 MB | ###########3 | 11%  python-3.12.9 | 34.7 MB | 7 | 1%  fastqc-0.12.1 | 11.1 MB | #######8 | 7%  openjdk-11.0.15 | 174.0 MB | 5 | 1% python-3.12.9 | 34.7 MB | ##9 | 3%  seqkit-2.12.0 | 6.5 MB | ########################6 | 23%  perl-5.32.1 | 12.7 MB | ##############################7 | 29%  fastqc-0.12.1 | 11.1 MB | ################5 | 16%  openjdk-11.0.15 | 174.0 MB | #2 | 1% python-3.12.9 | 34.7 MB | ####2 | 4%  seqkit-2.12.0 | 6.5 MB | ######################################8 | 37%  perl-5.32.1 | 12.7 MB | ####################################8 | 35%  openjdk-11.0.15 | 174.0 MB | #9 | 2% fastqc-0.12.1 | 11.1 MB | ######################################4 | 36%  perl-5.32.1 | 12.7 MB | ###################################################6 | 49%  seqkit-2.12.0 | 6.5 MB | #########################################################1 | 54%  python-3.12.9 | 34.7 MB | ########1 | 8%  openjdk-11.0.15 | 174.0 MB | ###1 | 3% fastqc-0.12.1 | 11.1 MB | ##############################################6 | 44%  seqkit-2.12.0 | 6.5 MB | ##############################################################################7 | 74%  python-3.12.9 | 34.7 MB | #############8 | 13%  fastqc-0.12.1 | 11.1 MB | ################################################################1 | 61%  perl-5.32.1 | 12.7 MB | ############################################################3 | 57%  openjdk-11.0.15 | 174.0 MB | ###6 | 3% seqkit-2.12.0 | 6.5 MB | ########################################################################################################## | 100%  seqkit-2.12.0 | 6.5 MB | ########################################################################################################## | 100%  openjdk-11.0.15 | 174.0 MB | ####9 | 5% python-3.12.9 | 34.7 MB | #####################1 | 20%  fastqc-0.12.1 | 11.1 MB | ###########################################################################9 | 72%  libstdcxx-15.2.0 | 5.6 MB | 2 | 0%  perl-5.32.1 | 12.7 MB | #############################################################################1 | 73%  seqkit-2.12.0 | 6.5 MB | ########################################################################################################## | 100%  python-3.12.9 | 34.7 MB | ########################3 | 23%  libstdcxx-15.2.0 | 5.6 MB | ##9 | 3%  openjdk-11.0.15 | 174.0 MB | #####6 | 5% fastqc-0.12.1 | 11.1 MB | ######################################################################################2 | 81%  python-3.12.9 | 34.7 MB | ##############################1 | 28%  perl-5.32.1 | 12.7 MB | ##########################################################################################5 | 85%  libstdcxx-15.2.0 | 5.6 MB | ######################2 | 21%  fastqc-0.12.1 | 11.1 MB | ########################################################################################################6 | 99%  openjdk-11.0.15 | 174.0 MB | ######4 | 6% python-3.12.9 | 34.7 MB | #################################7 | 32%  perl-5.32.1 | 12.7 MB | ########################################################################################################2 | 98%  fastqc-0.12.1 | 11.1 MB | ########################################################################################################## | 100%  openjdk-11.0.15 | 174.0 MB | #######6 | 7% libstdcxx-15.2.0 | 5.6 MB | ###########################################################6 | 56%  perl-5.32.1 | 12.7 MB | ########################################################################################################## | 100%  python-3.12.9 | 34.7 MB | ######################################4 | 36%  libstdcxx-15.2.0 | 5.6 MB | ################################################################################ | 76%  python-3.12.9 | 34.7 MB | ##########################################1 | 40%  libcups-2.3.3 | 4.3 MB | 3 | 0%  openjdk-11.0.15 | 174.0 MB | ########4 | 8% gettext-tools-0.25.1 | 3.5 MB | 4 | 0%  libstdcxx-15.2.0 | 5.6 MB | ###############################################################################################7 | 90%  python-3.12.9 | 34.7 MB | ##############################################3 | 44%  openjdk-11.0.15 | 174.0 MB | ######### | 9% libcups-2.3.3 | 4.3 MB | 7 | 1%  gettext-tools-0.25.1 | 3.5 MB | ######################################6 | 36%  libstdcxx-15.2.0 | 5.6 MB | ########################################################################################################## | 100%  openjdk-11.0.15 | 174.0 MB | #########7 | 9% libcups-2.3.3 | 4.3 MB | ##############################################8 | 44%  python-3.12.9 | 34.7 MB | #################################################9 | 47%  gettext-tools-0.25.1 | 3.5 MB | ##################################################################################4 | 78%  openjdk-11.0.15 | 174.0 MB | ##########5 | 10% libcups-2.3.3 | 4.3 MB | #################################################################### | 64%  gettext-tools-0.25.1 | 3.5 MB | ########################################################################################################## | 100%  tk-8.6.15 | 3.4 MB | 4 | 0%  python-3.12.9 | 34.7 MB | ######################################################8 | 52%  openjdk-11.0.15 | 174.0 MB | ###########2 | 11% libcups-2.3.3 | 4.3 MB | ###############################################################################################2 | 90%  libcups-2.3.3 | 4.3 MB | ########################################################################################################## | 100%  tk-8.6.15 | 3.4 MB | ##4 | 2%  openjdk-11.0.15 | 174.0 MB | ############ | 11% python-3.12.9 | 34.7 MB | ###########################################################7 | 56%  openssl-3.6.1 | 3.0 MB | 5 | 1%  tk-8.6.15 | 3.4 MB | ####8 | 5%  python-3.12.9 | 34.7 MB | ##############################################################9 | 59%  openjdk-11.0.15 | 174.0 MB | ############7 | 12% openssl-3.6.1 | 3.0 MB | ###################################################5 | 49%  tk-8.6.15 | 3.4 MB | ###########5 | 11%  python-3.12.9 | 34.7 MB | #################################################################8 | 62%  libglib-2.72.1 | 3.1 MB | 5 | 1%  openjdk-11.0.15 | 174.0 MB | #############5 | 13% openssl-3.6.1 | 3.0 MB | #################################################################################7 | 77%  tk-8.6.15 | 3.4 MB | ################3 | 15%  python-3.12.9 | 34.7 MB | ####################################################################6 | 65%  libglib-2.72.1 | 3.1 MB | ############################3 | 27%  openjdk-11.0.15 | 174.0 MB | ############## | 13% tk-8.6.15 | 3.4 MB | ######################## | 23%  libglib-2.72.1 | 3.1 MB | #######################################################################2 | 67%  openjdk-11.0.15 | 174.0 MB | ###############1 | 14% tk-8.6.15 | 3.4 MB | #############################3 | 28%  python-3.12.9 | 34.7 MB | ##########################################################################8 | 71%  openjdk-11.0.15 | 174.0 MB | ###############7 | 15% libglib-2.72.1 | 3.1 MB | ################################################################################################9 | 91%  python-3.12.9 | 34.7 MB | ###############################################################################6 | 75%  libglib-2.72.1 | 3.1 MB | ########################################################################################################## | 100%  tk-8.6.15 | 3.4 MB | ##################################1 | 32%  openssl-3.6.1 | 3.0 MB | ########################################################################################################## | 100%  openjdk-11.0.15 | 174.0 MB | ################4 | 16% python-3.12.9 | 34.7 MB | ####################################################################################6 | 80%  tk-8.6.15 | 3.4 MB | ##########################################8 | 40%  font-ttf-ubuntu-0.83 | 1.5 MB | # | 1%  openjdk-11.0.15 | 174.0 MB | #################5 | 17% tk-8.6.15 | 3.4 MB | ################################################1 | 45%  python-3.12.9 | 34.7 MB | ########################################################################################2 | 83%  font-ttf-ubuntu-0.83 | 1.5 MB | ########################################################8 | 54%  openjdk-11.0.15 | 174.0 MB | ##################6 | 18% tk-8.6.15 | 3.4 MB | #####################################################3 | 50%  python-3.12.9 | 34.7 MB | ############################################################################################9 | 88%  font-ttf-ubuntu-0.83 | 1.5 MB | ########################################################################################################## | 100%  openjdk-11.0.15 | 174.0 MB | ###################5 | 18% libmamba-1.5.11 | 1.9 MB | 8 | 1%  tk-8.6.15 | 3.4 MB | ##################################################################3 | 63%  python-3.12.9 | 34.7 MB | ################################################################################################## | 93%  bedtools-2.31.1 | 1.5 MB | # | 1%  libmamba-1.5.11 | 1.9 MB | #####3 | 5%  bedtools-2.31.1 | 1.5 MB | #######5 | 7%  fastqc-0.12.1 | 11.1 MB | ########################################################################################################## | 100%  tk-8.6.15 | 3.4 MB | #########################################################################6 | 69%  python-3.12.9 | 34.7 MB | ######################################################################################################1 | 96%  libmamba-1.5.11 | 1.9 MB | ########9 | 8%  openjdk-11.0.15 | 174.0 MB | ####################3 | 19% bedtools-2.31.1 | 1.5 MB | ########################################################################################################## | 100%  bedtools-2.31.1 | 1.5 MB | ########################################################################################################## | 100%  tk-8.6.15 | 3.4 MB | ###################################################################################7 | 79%  openjdk-11.0.15 | 174.0 MB | ###################### | 21% libmamba-1.5.11 | 1.9 MB | ##############################3 | 29%  tk-8.6.15 | 3.4 MB | ############################################################################################8 | 88%  libmamba-1.5.11 | 1.9 MB | ######################################################4 | 51%  harfbuzz-4.3.0 | 1.3 MB | #3 | 1%  tk-8.6.15 | 3.4 MB | ####################################################################################################5 | 95%  openjdk-11.0.15 | 174.0 MB | ######################9 | 22% libstdcxx-15.2.0 | 5.6 MB | ########################################################################################################## | 100%  libmamba-1.5.11 | 1.9 MB | ######################################################################################################5 | 97%  libmamba-1.5.11 | 1.9 MB | ########################################################################################################## | 100%  harfbuzz-4.3.0 | 1.3 MB | ##########5 | 10%  openjdk-11.0.15 | 174.0 MB | #######################7 | 22% tk-8.6.15 | 3.4 MB | ########################################################################################################## | 100%  pcre2-10.47 | 1.2 MB | #4 | 1%  harfbuzz-4.3.0 | 1.3 MB | ###########################################6 | 41%  openjdk-11.0.15 | 174.0 MB | ########################9 | 24% python-3.12.9 | 34.7 MB | ########################################################################################################## | 100%  python-3.12.9 | 34.7 MB | ########################################################################################################## | 100%  harfbuzz-4.3.0 | 1.3 MB | ############################################################8 | 57%  pcre2-10.47 | 1.2 MB | ########################1 | 23%  harfbuzz-4.3.0 | 1.3 MB | ########################################################################################################## | 100%  openjdk-11.0.15 | 174.0 MB | #########################8 | 24% pcre2-10.47 | 1.2 MB | ########################################################################################################## | 100%  conda-24.11.3 | 1.1 MB | #4 | 1%  conda-24.11.3 | 1.1 MB | #####9 | 6%  libgcc-15.2.0 | 1018 KB | #6 | 2%  openjdk-11.0.15 | 174.0 MB | ##########################7 | 25% sqlite-3.50.2 | 1.1 MB | #5 | 1%  libgcc-15.2.0 | 1018 KB | ########################################################################################################## | 100%  sqlite-3.50.2 | 1.1 MB | ########################################################################################################## | 100%  conda-24.11.3 | 1.1 MB | ################2 | 15%  openjdk-11.0.15 | 174.0 MB | ############################5 | 27% libarchive-3.7.7 | 846 KB | ## | 2%  xorg-libx11-1.8.12 | 816 KB | ## | 2%  gettext-tools-0.25.1 | 3.5 MB | ########################################################################################################## | 100%  conda-24.11.3 | 1.1 MB | #########################1 | 24%  xorg-libx11-1.8.12 | 816 KB | ##########3 | 10%  libarchive-3.7.7 | 846 KB | ################## | 17%  libarchive-3.7.7 | 846 KB | ########################################################################################################## | 100%  xorg-libx11-1.8.12 | 816 KB | ########################################################################################################## | 100%  openjdk-11.0.15 | 174.0 MB | #############################5 | 28% cairo-1.16.0 | 1.2 MB | #4 | 1%  conda-24.11.3 | 1.1 MB | ############################################4 | 42%  openjdk-11.0.15 | 174.0 MB | ##############################8 | 29% libiconv-1.18 | 772 KB | ##1 | 2%  libcups-2.3.3 | 4.3 MB | ########################################################################################################## | 100%  ... (more hidden) ... cairo-1.16.0 | 1.2 MB | ########## | 9%  conda-24.11.3 | 1.1 MB | ###########################################################2 | 56%  ... (more hidden) ... openjdk-11.0.15 | 174.0 MB | ###############################9 | 30% openjdk-11.0.15 | 174.0 MB | ################################8 | 31% conda-24.11.3 | 1.1 MB | #####################################################################5 | 66%  cairo-1.16.0 | 1.2 MB | ########################################2 | 38%  perl-5.32.1 | 12.7 MB | ########################################################################################################## | 100%  conda-24.11.3 | 1.1 MB | ################################################################################################2 | 91%  openjdk-11.0.15 | 174.0 MB | #################################7 | 32% cairo-1.16.0 | 1.2 MB | ###################################################################################################### | 96%  conda-24.11.3 | 1.1 MB | ########################################################################################################## | 100%  libiconv-1.18 | 772 KB | ############################################################################################3 | 87%  libiconv-1.18 | 772 KB | ########################################################################################################## | 100%  openjdk-11.0.15 | 174.0 MB | ##################################6 | 33% cairo-1.16.0 | 1.2 MB | ########################################################################################################## | 100%  openjdk-11.0.15 | 174.0 MB | ####################################2 | 34% openssl-3.6.1 | 3.0 MB | ########################################################################################################## | 100%  openjdk-11.0.15 | 174.0 MB | #####################################4 | 35% font-ttf-ubuntu-0.83 | 1.5 MB | ########################################################################################################## | 100%  font-ttf-ubuntu-0.83 | 1.5 MB | ########################################################################################################## | 100%  openjdk-11.0.15 | 174.0 MB | ######################################5 | 36% openjdk-11.0.15 | 174.0 MB | #######################################7 | 38% openjdk-11.0.15 | 174.0 MB | ########################################8 | 39% openjdk-11.0.15 | 174.0 MB | ##########################################1 | 40% bedtools-2.31.1 | 1.5 MB | ########################################################################################################## | 100%  openjdk-11.0.15 | 174.0 MB | ############################################2 | 42% libglib-2.72.1 | 3.1 MB | ########################################################################################################## | 100%  libmamba-1.5.11 | 1.9 MB | ########################################################################################################## | 100%  openjdk-11.0.15 | 174.0 MB | #############################################5 | 43% openjdk-11.0.15 | 174.0 MB | ##############################################7 | 44% openjdk-11.0.15 | 174.0 MB | ###############################################9 | 45% openjdk-11.0.15 | 174.0 MB | ################################################9 | 46% openjdk-11.0.15 | 174.0 MB | #################################################9 | 47% openjdk-11.0.15 | 174.0 MB | ################################################### | 48% tk-8.6.15 | 3.4 MB | ########################################################################################################## | 100%  openjdk-11.0.15 | 174.0 MB | ###################################################9 | 49% harfbuzz-4.3.0 | 1.3 MB | ########################################################################################################## | 100%  harfbuzz-4.3.0 | 1.3 MB | ########################################################################################################## | 100%  openjdk-11.0.15 | 174.0 MB | ####################################################7 | 50% openjdk-11.0.15 | 174.0 MB | ######################################################6 | 52% openjdk-11.0.15 | 174.0 MB | #######################################################5 | 52% pcre2-10.47 | 1.2 MB | ########################################################################################################## | 100%  pcre2-10.47 | 1.2 MB | ########################################################################################################## | 100%  openjdk-11.0.15 | 174.0 MB | ########################################################4 | 53% libgcc-15.2.0 | 1018 KB | ########################################################################################################## | 100%  libgcc-15.2.0 | 1018 KB | ########################################################################################################## | 100%  openjdk-11.0.15 | 174.0 MB | #########################################################6 | 54% sqlite-3.50.2 | 1.1 MB | ########################################################################################################## | 100%  sqlite-3.50.2 | 1.1 MB | ########################################################################################################## | 100%  openjdk-11.0.15 | 174.0 MB | ##########################################################5 | 55% libarchive-3.7.7 | 846 KB | ########################################################################################################## | 100%  libarchive-3.7.7 | 846 KB | ########################################################################################################## | 100%  openjdk-11.0.15 | 174.0 MB | ############################################################4 | 57% openjdk-11.0.15 | 174.0 MB | #############################################################4 | 58% openjdk-11.0.15 | 174.0 MB | ##############################################################7 | 59% openjdk-11.0.15 | 174.0 MB | ################################################################3 | 61% xorg-libx11-1.8.12 | 816 KB | ########################################################################################################## | 100%  xorg-libx11-1.8.12 | 816 KB | ########################################################################################################## | 100%  openjdk-11.0.15 | 174.0 MB | #################################################################5 | 62% ... (more hidden) ... ... (more hidden) ... openjdk-11.0.15 | 174.0 MB | ##################################################################9 | 63% openjdk-11.0.15 | 174.0 MB | ####################################################################1 | 64% openjdk-11.0.15 | 174.0 MB | #####################################################################3 | 65% openjdk-11.0.15 | 174.0 MB | #######################################################################3 | 67% openjdk-11.0.15 | 174.0 MB | ########################################################################8 | 69% openjdk-11.0.15 | 174.0 MB | ##########################################################################1 | 70% openjdk-11.0.15 | 174.0 MB | ###########################################################################4 | 71% openjdk-11.0.15 | 174.0 MB | #############################################################################1 | 73% conda-24.11.3 | 1.1 MB | ########################################################################################################## | 100%  python-3.12.9 | 34.7 MB | ########################################################################################################## | 100%  libiconv-1.18 | 772 KB | ########################################################################################################## | 100%  libiconv-1.18 | 772 KB | ########################################################################################################## | 100%  openjdk-11.0.15 | 174.0 MB | ##############################################################################4 | 74% cairo-1.16.0 | 1.2 MB | ########################################################################################################## | 100%  openjdk-11.0.15 | 174.0 MB | ###############################################################################5 | 75% openjdk-11.0.15 | 174.0 MB | #################################################################################4 | 77% openjdk-11.0.15 | 174.0 MB | ##################################################################################6 | 78% openjdk-11.0.15 | 174.0 MB | ###################################################################################8 | 79% openjdk-11.0.15 | 174.0 MB | ####################################################################################9 | 80% openjdk-11.0.15 | 174.0 MB | ###################################################################################### | 81% openjdk-11.0.15 | 174.0 MB | #######################################################################################9 | 83% openjdk-11.0.15 | 174.0 MB | #########################################################################################6 | 85% openjdk-11.0.15 | 174.0 MB | ###########################################################################################3 | 86% openjdk-11.0.15 | 174.0 MB | ############################################################################################4 | 87% openjdk-11.0.15 | 174.0 MB | #############################################################################################9 | 89% openjdk-11.0.15 | 174.0 MB | ###############################################################################################5 | 90% openjdk-11.0.15 | 174.0 MB | #################################################################################################2 | 92% openjdk-11.0.15 | 174.0 MB | ##################################################################################################5 | 93% openjdk-11.0.15 | 174.0 MB | ###################################################################################################8 | 94% openjdk-11.0.15 | 174.0 MB | #####################################################################################################7 | 96% openjdk-11.0.15 | 174.0 MB | #######################################################################################################7 | 98% openjdk-11.0.15 | 174.0 MB | #########################################################################################################2 | 99% openjdk-11.0.15 | 174.0 MB | ########################################################################################################## | 100% openjdk-11.0.15 | 174.0 MB | ########################################################################################################## | 100%                                                                                Preparing transaction: | / - \ | done Verifying transaction: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done Executing transaction: | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done [?2004h(base) gskoksharova@genedev2:/sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM$ fastqc -t 6 *.fq.gz *.fq.gz*.fq.gz *.fq.gz *.fq.gz*.fq.gz [?2004l application/gzip application/gzip Started analysis of Read1-10mg.fq.gz Analysis complete for Read1-10mg.fq.gz Failed to process file Read1-10mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read1-10mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) application/gzip application/gzip application/gzip Started analysis of Read1-11mg.fq.gz Approx 5% complete for Read1-11mg.fq.gz application/gzip application/gzip application/gzip application/gzip Approx 10% complete for Read1-11mg.fq.gz Approx 15% complete for Read1-11mg.fq.gz application/gzip Approx 20% complete for Read1-11mg.fq.gz application/gzip Approx 25% complete for Read1-11mg.fq.gz application/gzip Approx 30% complete for Read1-11mg.fq.gz application/gzip Approx 35% complete for Read1-11mg.fq.gz application/gzip Approx 40% complete for Read1-11mg.fq.gz application/gzip Approx 45% complete for Read1-11mg.fq.gz Approx 50% complete for Read1-11mg.fq.gz application/gzip Approx 55% complete for Read1-11mg.fq.gz application/gzip Approx 60% complete for Read1-11mg.fq.gz application/gzip application/gzip Approx 65% complete for Read1-11mg.fq.gz Approx 70% complete for Read1-11mg.fq.gz application/gzip Approx 75% complete for Read1-11mg.fq.gz application/gzip Approx 80% complete for Read1-11mg.fq.gz application/gzip Approx 85% complete for Read1-11mg.fq.gz application/gzip Approx 90% complete for Read1-11mg.fq.gz application/gzip application/gzip application/gzip Approx 95% complete for Read1-11mg.fq.gz application/gzip Analysis complete for Read1-11mg.fq.gz Failed to process file Read1-11mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read1-11mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) application/gzip application/gzip Started analysis of Read1-12mg.fq.gz application/gzip application/gzip application/gzip application/gzip application/gzip Approx 5% complete for Read1-12mg.fq.gz Approx 10% complete for Read1-12mg.fq.gz Approx 15% complete for Read1-12mg.fq.gz Approx 20% complete for Read1-12mg.fq.gz Approx 25% complete for Read1-12mg.fq.gz Approx 30% complete for Read1-12mg.fq.gz Approx 35% complete for Read1-12mg.fq.gz Approx 40% complete for Read1-12mg.fq.gz Approx 45% complete for Read1-12mg.fq.gz Approx 50% complete for Read1-12mg.fq.gz Approx 55% complete for Read1-12mg.fq.gz Approx 60% complete for Read1-12mg.fq.gz Approx 65% complete for Read1-12mg.fq.gz Approx 70% complete for Read1-12mg.fq.gz Approx 75% complete for Read1-12mg.fq.gz Approx 80% complete for Read1-12mg.fq.gz Approx 85% complete for Read1-12mg.fq.gz Approx 90% complete for Read1-12mg.fq.gz Approx 95% complete for Read1-12mg.fq.gz Analysis complete for Read1-12mg.fq.gz Failed to process file Read1-12mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read1-12mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) Started analysis of Read1-13mg.fq.gz Approx 5% complete for Read1-13mg.fq.gz Approx 10% complete for Read1-13mg.fq.gz Approx 15% complete for Read1-13mg.fq.gz Approx 20% complete for Read1-13mg.fq.gz Approx 25% complete for Read1-13mg.fq.gz Approx 30% complete for Read1-13mg.fq.gz Approx 35% complete for Read1-13mg.fq.gz Approx 40% complete for Read1-13mg.fq.gz Approx 45% complete for Read1-13mg.fq.gz Approx 50% complete for Read1-13mg.fq.gz Approx 55% complete for Read1-13mg.fq.gz Approx 60% complete for Read1-13mg.fq.gz Approx 65% complete for Read1-13mg.fq.gz Approx 70% complete for Read1-13mg.fq.gz Approx 75% complete for Read1-13mg.fq.gz Approx 80% complete for Read1-13mg.fq.gz Approx 85% complete for Read1-13mg.fq.gz Approx 90% complete for Read1-13mg.fq.gz Approx 95% complete for Read1-13mg.fq.gz Analysis complete for Read1-13mg.fq.gz Failed to process file Read1-13mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read1-13mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) Started analysis of Read1-14mg.fq.gz Approx 5% complete for Read1-14mg.fq.gz Approx 10% complete for Read1-14mg.fq.gz Approx 15% complete for Read1-14mg.fq.gz Approx 20% complete for Read1-14mg.fq.gz Approx 25% complete for Read1-14mg.fq.gz Approx 30% complete for Read1-14mg.fq.gz Approx 35% complete for Read1-14mg.fq.gz Approx 40% complete for Read1-14mg.fq.gz Approx 45% complete for Read1-14mg.fq.gz Approx 50% complete for Read1-14mg.fq.gz Approx 55% complete for Read1-14mg.fq.gz Approx 60% complete for Read1-14mg.fq.gz Approx 65% complete for Read1-14mg.fq.gz Approx 70% complete for Read1-14mg.fq.gz Approx 75% complete for Read1-14mg.fq.gz Approx 80% complete for Read1-14mg.fq.gz Approx 85% complete for Read1-14mg.fq.gz Approx 90% complete for Read1-14mg.fq.gz Approx 95% complete for Read1-14mg.fq.gz Analysis complete for Read1-14mg.fq.gz Failed to process file Read1-14mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read1-14mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) Started analysis of Read1-15mg.fq.gz Analysis complete for Read1-15mg.fq.gz Failed to process file Read1-15mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read1-15mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) Started analysis of Read1-16mg.fq.gz Analysis complete for Read1-16mg.fq.gz Failed to process file Read1-16mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read1-16mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) Started analysis of Read1-17mg.fq.gz Analysis complete for Read1-17mg.fq.gz Failed to process file Read1-17mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read1-17mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) Started analysis of Read1-1mg.fq.gz Approx 5% complete for Read1-1mg.fq.gz Approx 10% complete for Read1-1mg.fq.gz Approx 15% complete for Read1-1mg.fq.gz Approx 20% complete for Read1-1mg.fq.gz Approx 25% complete for Read1-1mg.fq.gz Approx 30% complete for Read1-1mg.fq.gz Approx 35% complete for Read1-1mg.fq.gz Approx 40% complete for Read1-1mg.fq.gz Approx 45% complete for Read1-1mg.fq.gz Approx 50% complete for Read1-1mg.fq.gz Approx 55% complete for Read1-1mg.fq.gz Approx 60% complete for Read1-1mg.fq.gz Approx 65% complete for Read1-1mg.fq.gz Approx 70% complete for Read1-1mg.fq.gz Approx 75% complete for Read1-1mg.fq.gz Approx 80% complete for Read1-1mg.fq.gz Approx 85% complete for Read1-1mg.fq.gz Approx 90% complete for Read1-1mg.fq.gz Approx 95% complete for Read1-1mg.fq.gz Analysis complete for Read1-1mg.fq.gz Failed to process file Read1-1mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read1-1mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) Started analysis of Read1-2mg.fq.gz Approx 5% complete for Read1-2mg.fq.gz Approx 10% complete for Read1-2mg.fq.gz Approx 15% complete for Read1-2mg.fq.gz Approx 20% complete for Read1-2mg.fq.gz Approx 25% complete for Read1-2mg.fq.gz Approx 30% complete for Read1-2mg.fq.gz Approx 35% complete for Read1-2mg.fq.gz Approx 40% complete for Read1-2mg.fq.gz Approx 45% complete for Read1-2mg.fq.gz Approx 50% complete for Read1-2mg.fq.gz Approx 55% complete for Read1-2mg.fq.gz Approx 60% complete for Read1-2mg.fq.gz Approx 65% complete for Read1-2mg.fq.gz Approx 70% complete for Read1-2mg.fq.gz Approx 75% complete for Read1-2mg.fq.gz Approx 80% complete for Read1-2mg.fq.gz Approx 85% complete for Read1-2mg.fq.gz Approx 90% complete for Read1-2mg.fq.gz Approx 95% complete for Read1-2mg.fq.gz Analysis complete for Read1-2mg.fq.gz Failed to process file Read1-2mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read1-2mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) Started analysis of Read1-3mg.fq.gz Approx 5% complete for Read1-3mg.fq.gz Approx 10% complete for Read1-3mg.fq.gz Approx 15% complete for Read1-3mg.fq.gz Approx 20% complete for Read1-3mg.fq.gz Approx 25% complete for Read1-3mg.fq.gz Approx 30% complete for Read1-3mg.fq.gz Approx 35% complete for Read1-3mg.fq.gz Approx 40% complete for Read1-3mg.fq.gz Approx 45% complete for Read1-3mg.fq.gz Approx 50% complete for Read1-3mg.fq.gz Approx 55% complete for Read1-3mg.fq.gz Approx 60% complete for Read1-3mg.fq.gz Approx 65% complete for Read1-3mg.fq.gz Approx 70% complete for Read1-3mg.fq.gz Approx 75% complete for Read1-3mg.fq.gz Approx 80% complete for Read1-3mg.fq.gz Approx 85% complete for Read1-3mg.fq.gz Approx 90% complete for Read1-3mg.fq.gz Approx 95% complete for Read1-3mg.fq.gz Analysis complete for Read1-3mg.fq.gz Failed to process file Read1-3mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read1-3mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) Started analysis of Read1-4mg.fq.gz Approx 5% complete for Read1-4mg.fq.gz Approx 10% complete for Read1-4mg.fq.gz Approx 15% complete for Read1-4mg.fq.gz Approx 20% complete for Read1-4mg.fq.gz Approx 25% complete for Read1-4mg.fq.gz Approx 30% complete for Read1-4mg.fq.gz Approx 35% complete for Read1-4mg.fq.gz Approx 40% complete for Read1-4mg.fq.gz Approx 45% complete for Read1-4mg.fq.gz Approx 50% complete for Read1-4mg.fq.gz Approx 55% complete for Read1-4mg.fq.gz Approx 60% complete for Read1-4mg.fq.gz Approx 65% complete for Read1-4mg.fq.gz Approx 70% complete for Read1-4mg.fq.gz Approx 75% complete for Read1-4mg.fq.gz Approx 80% complete for Read1-4mg.fq.gz Approx 85% complete for Read1-4mg.fq.gz Approx 90% complete for Read1-4mg.fq.gz Approx 95% complete for Read1-4mg.fq.gz Analysis complete for Read1-4mg.fq.gz Failed to process file Read1-4mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read1-4mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) Started analysis of Read1-5mg.fq.gz Approx 5% complete for Read1-5mg.fq.gz Approx 10% complete for Read1-5mg.fq.gz Approx 15% complete for Read1-5mg.fq.gz Approx 20% complete for Read1-5mg.fq.gz Approx 25% complete for Read1-5mg.fq.gz Approx 30% complete for Read1-5mg.fq.gz Approx 35% complete for Read1-5mg.fq.gz Approx 40% complete for Read1-5mg.fq.gz Approx 45% complete for Read1-5mg.fq.gz Approx 50% complete for Read1-5mg.fq.gz Approx 55% complete for Read1-5mg.fq.gz Approx 60% complete for Read1-5mg.fq.gz Approx 65% complete for Read1-5mg.fq.gz Approx 70% complete for Read1-5mg.fq.gz Approx 75% complete for Read1-5mg.fq.gz Approx 80% complete for Read1-5mg.fq.gz Approx 85% complete for Read1-5mg.fq.gz Approx 90% complete for Read1-5mg.fq.gz Approx 95% complete for Read1-5mg.fq.gz Analysis complete for Read1-5mg.fq.gz Failed to process file Read1-5mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read1-5mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) Started analysis of Read1-6mg.fq.gz Approx 5% complete for Read1-6mg.fq.gz Approx 10% complete for Read1-6mg.fq.gz Approx 15% complete for Read1-6mg.fq.gz Approx 20% complete for Read1-6mg.fq.gz Approx 25% complete for Read1-6mg.fq.gz Approx 30% complete for Read1-6mg.fq.gz Approx 35% complete for Read1-6mg.fq.gz Approx 40% complete for Read1-6mg.fq.gz Approx 45% complete for Read1-6mg.fq.gz Approx 50% complete for Read1-6mg.fq.gz Approx 55% complete for Read1-6mg.fq.gz Approx 60% complete for Read1-6mg.fq.gz Approx 65% complete for Read1-6mg.fq.gz Approx 70% complete for Read1-6mg.fq.gz Approx 75% complete for Read1-6mg.fq.gz Approx 80% complete for Read1-6mg.fq.gz Approx 85% complete for Read1-6mg.fq.gz Approx 90% complete for Read1-6mg.fq.gz Approx 95% complete for Read1-6mg.fq.gz Analysis complete for Read1-6mg.fq.gz Failed to process file Read1-6mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read1-6mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) Started analysis of Read1-7mg.fq.gz Approx 5% complete for Read1-7mg.fq.gz Approx 10% complete for Read1-7mg.fq.gz Approx 15% complete for Read1-7mg.fq.gz Approx 20% complete for Read1-7mg.fq.gz Approx 25% complete for Read1-7mg.fq.gz Approx 30% complete for Read1-7mg.fq.gz Approx 35% complete for Read1-7mg.fq.gz Approx 40% complete for Read1-7mg.fq.gz Approx 45% complete for Read1-7mg.fq.gz Approx 50% complete for Read1-7mg.fq.gz Approx 55% complete for Read1-7mg.fq.gz Approx 60% complete for Read1-7mg.fq.gz Approx 65% complete for Read1-7mg.fq.gz Approx 70% complete for Read1-7mg.fq.gz Approx 75% complete for Read1-7mg.fq.gz Approx 80% complete for Read1-7mg.fq.gz Approx 85% complete for Read1-7mg.fq.gz Approx 90% complete for Read1-7mg.fq.gz Approx 95% complete for Read1-7mg.fq.gz Analysis complete for Read1-7mg.fq.gz Failed to process file Read1-7mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read1-7mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) Started analysis of Read1-8gm.fq.gz Approx 5% complete for Read1-8gm.fq.gz Approx 10% complete for Read1-8gm.fq.gz Approx 15% complete for Read1-8gm.fq.gz Approx 20% complete for Read1-8gm.fq.gz Approx 25% complete for Read1-8gm.fq.gz Approx 30% complete for Read1-8gm.fq.gz Approx 35% complete for Read1-8gm.fq.gz Approx 40% complete for Read1-8gm.fq.gz Approx 45% complete for Read1-8gm.fq.gz Approx 50% complete for Read1-8gm.fq.gz Approx 55% complete for Read1-8gm.fq.gz Approx 60% complete for Read1-8gm.fq.gz Approx 65% complete for Read1-8gm.fq.gz Approx 70% complete for Read1-8gm.fq.gz Approx 75% complete for Read1-8gm.fq.gz Approx 80% complete for Read1-8gm.fq.gz Approx 85% complete for Read1-8gm.fq.gz Approx 90% complete for Read1-8gm.fq.gz Approx 95% complete for Read1-8gm.fq.gz Analysis complete for Read1-8gm.fq.gz Failed to process file Read1-8gm.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read1-8gm_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) Started analysis of Read1-9mg.fq.gz Approx 5% complete for Read1-9mg.fq.gz Approx 10% complete for Read1-9mg.fq.gz Approx 15% complete for Read1-9mg.fq.gz Approx 20% complete for Read1-9mg.fq.gz Approx 25% complete for Read1-9mg.fq.gz Approx 30% complete for Read1-9mg.fq.gz Approx 35% complete for Read1-9mg.fq.gz Approx 40% complete for Read1-9mg.fq.gz Approx 45% complete for Read1-9mg.fq.gz Approx 50% complete for Read1-9mg.fq.gz Approx 55% complete for Read1-9mg.fq.gz Approx 60% complete for Read1-9mg.fq.gz Approx 65% complete for Read1-9mg.fq.gz Approx 70% complete for Read1-9mg.fq.gz Approx 75% complete for Read1-9mg.fq.gz Approx 80% complete for Read1-9mg.fq.gz Approx 85% complete for Read1-9mg.fq.gz Approx 90% complete for Read1-9mg.fq.gz Approx 95% complete for Read1-9mg.fq.gz Analysis complete for Read1-9mg.fq.gz Failed to process file Read1-9mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read1-9mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) Started analysis of Read2-10mg.fq.gz Analysis complete for Read2-10mg.fq.gz Failed to process file Read2-10mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read2-10mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) Started analysis of Read2-11mg.fq.gz Approx 5% complete for Read2-11mg.fq.gz Approx 10% complete for Read2-11mg.fq.gz Approx 15% complete for Read2-11mg.fq.gz Approx 20% complete for Read2-11mg.fq.gz Approx 25% complete for Read2-11mg.fq.gz Approx 30% complete for Read2-11mg.fq.gz Approx 35% complete for Read2-11mg.fq.gz Approx 40% complete for Read2-11mg.fq.gz Approx 45% complete for Read2-11mg.fq.gz Approx 50% complete for Read2-11mg.fq.gz Approx 55% complete for Read2-11mg.fq.gz Approx 60% complete for Read2-11mg.fq.gz Approx 65% complete for Read2-11mg.fq.gz Approx 70% complete for Read2-11mg.fq.gz Approx 75% complete for Read2-11mg.fq.gz Approx 80% complete for Read2-11mg.fq.gz Approx 85% complete for Read2-11mg.fq.gz Approx 90% complete for Read2-11mg.fq.gz Approx 95% complete for Read2-11mg.fq.gz Analysis complete for Read2-11mg.fq.gz Failed to process file Read2-11mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read2-11mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) Started analysis of Read2-12mg.fq.gz Approx 5% complete for Read2-12mg.fq.gz Approx 10% complete for Read2-12mg.fq.gz Approx 15% complete for Read2-12mg.fq.gz Approx 20% complete for Read2-12mg.fq.gz Approx 25% complete for Read2-12mg.fq.gz Approx 30% complete for Read2-12mg.fq.gz Approx 35% complete for Read2-12mg.fq.gz Approx 40% complete for Read2-12mg.fq.gz Approx 45% complete for Read2-12mg.fq.gz Approx 50% complete for Read2-12mg.fq.gz Approx 55% complete for Read2-12mg.fq.gz Approx 60% complete for Read2-12mg.fq.gz Approx 65% complete for Read2-12mg.fq.gz Approx 70% complete for Read2-12mg.fq.gz Approx 75% complete for Read2-12mg.fq.gz Approx 80% complete for Read2-12mg.fq.gz Approx 85% complete for Read2-12mg.fq.gz Approx 90% complete for Read2-12mg.fq.gz Approx 95% complete for Read2-12mg.fq.gz Analysis complete for Read2-12mg.fq.gz Failed to process file Read2-12mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read2-12mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) Started analysis of Read2-13mg.fq.gz Approx 5% complete for Read2-13mg.fq.gz Approx 10% complete for Read2-13mg.fq.gz Approx 15% complete for Read2-13mg.fq.gz Approx 20% complete for Read2-13mg.fq.gz Approx 25% complete for Read2-13mg.fq.gz Approx 30% complete for Read2-13mg.fq.gz Approx 35% complete for Read2-13mg.fq.gz Approx 40% complete for Read2-13mg.fq.gz Approx 45% complete for Read2-13mg.fq.gz Approx 50% complete for Read2-13mg.fq.gz Approx 55% complete for Read2-13mg.fq.gz Approx 60% complete for Read2-13mg.fq.gz Approx 65% complete for Read2-13mg.fq.gz Approx 70% complete for Read2-13mg.fq.gz Approx 75% complete for Read2-13mg.fq.gz Approx 80% complete for Read2-13mg.fq.gz Approx 85% complete for Read2-13mg.fq.gz Approx 90% complete for Read2-13mg.fq.gz Approx 95% complete for Read2-13mg.fq.gz Analysis complete for Read2-13mg.fq.gz Failed to process file Read2-13mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read2-13mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) Started analysis of Read2-14mg.fq.gz Approx 5% complete for Read2-14mg.fq.gz Approx 10% complete for Read2-14mg.fq.gz Approx 15% complete for Read2-14mg.fq.gz Approx 20% complete for Read2-14mg.fq.gz Approx 25% complete for Read2-14mg.fq.gz Approx 30% complete for Read2-14mg.fq.gz Approx 35% complete for Read2-14mg.fq.gz Approx 40% complete for Read2-14mg.fq.gz Approx 45% complete for Read2-14mg.fq.gz Approx 50% complete for Read2-14mg.fq.gz Approx 55% complete for Read2-14mg.fq.gz Approx 60% complete for Read2-14mg.fq.gz Approx 65% complete for Read2-14mg.fq.gz Approx 70% complete for Read2-14mg.fq.gz Approx 75% complete for Read2-14mg.fq.gz Approx 80% complete for Read2-14mg.fq.gz Approx 85% complete for Read2-14mg.fq.gz Approx 90% complete for Read2-14mg.fq.gz Approx 95% complete for Read2-14mg.fq.gz Analysis complete for Read2-14mg.fq.gz Failed to process file Read2-14mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read2-14mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) Started analysis of Read2-15mg.fq.gz Analysis complete for Read2-15mg.fq.gz Failed to process file Read2-15mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read2-15mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) Started analysis of Read2-16mg.fq.gz Analysis complete for Read2-16mg.fq.gz Failed to process file Read2-16mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read2-16mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) Started analysis of Read2-17mg.fq.gz Analysis complete for Read2-17mg.fq.gz Failed to process file Read2-17mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read2-17mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) Started analysis of Read2-1mg.fq.gz Approx 5% complete for Read2-1mg.fq.gz Approx 10% complete for Read2-1mg.fq.gz Approx 15% complete for Read2-1mg.fq.gz Approx 20% complete for Read2-1mg.fq.gz Approx 25% complete for Read2-1mg.fq.gz Approx 30% complete for Read2-1mg.fq.gz Approx 35% complete for Read2-1mg.fq.gz Approx 40% complete for Read2-1mg.fq.gz Approx 45% complete for Read2-1mg.fq.gz Approx 50% complete for Read2-1mg.fq.gz Approx 55% complete for Read2-1mg.fq.gz Approx 60% complete for Read2-1mg.fq.gz Approx 65% complete for Read2-1mg.fq.gz Approx 70% complete for Read2-1mg.fq.gz Approx 75% complete for Read2-1mg.fq.gz Approx 80% complete for Read2-1mg.fq.gz Approx 85% complete for Read2-1mg.fq.gz Approx 90% complete for Read2-1mg.fq.gz Approx 95% complete for Read2-1mg.fq.gz Analysis complete for Read2-1mg.fq.gz Failed to process file Read2-1mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read2-1mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) Started analysis of Read2-2mg.fq.gz Approx 5% complete for Read2-2mg.fq.gz Approx 10% complete for Read2-2mg.fq.gz Approx 15% complete for Read2-2mg.fq.gz Approx 20% complete for Read2-2mg.fq.gz Approx 25% complete for Read2-2mg.fq.gz Approx 30% complete for Read2-2mg.fq.gz Approx 35% complete for Read2-2mg.fq.gz Approx 40% complete for Read2-2mg.fq.gz Approx 45% complete for Read2-2mg.fq.gz Approx 50% complete for Read2-2mg.fq.gz Approx 55% complete for Read2-2mg.fq.gz Approx 60% complete for Read2-2mg.fq.gz Approx 65% complete for Read2-2mg.fq.gz Approx 70% complete for Read2-2mg.fq.gz Approx 75% complete for Read2-2mg.fq.gz Approx 80% complete for Read2-2mg.fq.gz Approx 85% complete for Read2-2mg.fq.gz Approx 90% complete for Read2-2mg.fq.gz Approx 95% complete for Read2-2mg.fq.gz Analysis complete for Read2-2mg.fq.gz Failed to process file Read2-2mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read2-2mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) Started analysis of Read2-3mg.fq.gz Approx 5% complete for Read2-3mg.fq.gz Approx 10% complete for Read2-3mg.fq.gz Approx 15% complete for Read2-3mg.fq.gz Approx 20% complete for Read2-3mg.fq.gz Approx 25% complete for Read2-3mg.fq.gz Approx 30% complete for Read2-3mg.fq.gz Approx 35% complete for Read2-3mg.fq.gz Approx 40% complete for Read2-3mg.fq.gz Approx 45% complete for Read2-3mg.fq.gz Approx 50% complete for Read2-3mg.fq.gz Approx 55% complete for Read2-3mg.fq.gz Approx 60% complete for Read2-3mg.fq.gz Approx 65% complete for Read2-3mg.fq.gz Approx 70% complete for Read2-3mg.fq.gz Approx 75% complete for Read2-3mg.fq.gz Approx 80% complete for Read2-3mg.fq.gz Approx 85% complete for Read2-3mg.fq.gz Approx 90% complete for Read2-3mg.fq.gz Approx 95% complete for Read2-3mg.fq.gz Analysis complete for Read2-3mg.fq.gz Failed to process file Read2-3mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read2-3mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) Started analysis of Read2-4mg.fq.gz Approx 5% complete for Read2-4mg.fq.gz Approx 10% complete for Read2-4mg.fq.gz Approx 15% complete for Read2-4mg.fq.gz Approx 20% complete for Read2-4mg.fq.gz Approx 25% complete for Read2-4mg.fq.gz Approx 30% complete for Read2-4mg.fq.gz Approx 35% complete for Read2-4mg.fq.gz Approx 40% complete for Read2-4mg.fq.gz Approx 45% complete for Read2-4mg.fq.gz Approx 50% complete for Read2-4mg.fq.gz Approx 55% complete for Read2-4mg.fq.gz Approx 60% complete for Read2-4mg.fq.gz Approx 65% complete for Read2-4mg.fq.gz Approx 70% complete for Read2-4mg.fq.gz Approx 75% complete for Read2-4mg.fq.gz Approx 80% complete for Read2-4mg.fq.gz Approx 85% complete for Read2-4mg.fq.gz Approx 90% complete for Read2-4mg.fq.gz Approx 95% complete for Read2-4mg.fq.gz Analysis complete for Read2-4mg.fq.gz Failed to process file Read2-4mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read2-4mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) Started analysis of Read2-5mg.fq.gz Approx 5% complete for Read2-5mg.fq.gz Approx 10% complete for Read2-5mg.fq.gz Approx 15% complete for Read2-5mg.fq.gz Approx 20% complete for Read2-5mg.fq.gz Approx 25% complete for Read2-5mg.fq.gz Approx 30% complete for Read2-5mg.fq.gz Approx 35% complete for Read2-5mg.fq.gz Approx 40% complete for Read2-5mg.fq.gz Approx 45% complete for Read2-5mg.fq.gz Approx 50% complete for Read2-5mg.fq.gz Approx 55% complete for Read2-5mg.fq.gz Approx 60% complete for Read2-5mg.fq.gz Approx 65% complete for Read2-5mg.fq.gz Approx 70% complete for Read2-5mg.fq.gz Approx 75% complete for Read2-5mg.fq.gz Approx 80% complete for Read2-5mg.fq.gz Approx 85% complete for Read2-5mg.fq.gz Approx 90% complete for Read2-5mg.fq.gz Approx 95% complete for Read2-5mg.fq.gz Analysis complete for Read2-5mg.fq.gz Failed to process file Read2-5mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read2-5mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) Started analysis of Read2-6mg.fq.gz Approx 5% complete for Read2-6mg.fq.gz Approx 10% complete for Read2-6mg.fq.gz Approx 15% complete for Read2-6mg.fq.gz Approx 20% complete for Read2-6mg.fq.gz Approx 25% complete for Read2-6mg.fq.gz Approx 30% complete for Read2-6mg.fq.gz Approx 35% complete for Read2-6mg.fq.gz Approx 40% complete for Read2-6mg.fq.gz Approx 45% complete for Read2-6mg.fq.gz Approx 50% complete for Read2-6mg.fq.gz Approx 55% complete for Read2-6mg.fq.gz Approx 60% complete for Read2-6mg.fq.gz Approx 65% complete for Read2-6mg.fq.gz Approx 70% complete for Read2-6mg.fq.gz Approx 75% complete for Read2-6mg.fq.gz Approx 80% complete for Read2-6mg.fq.gz Approx 85% complete for Read2-6mg.fq.gz Approx 90% complete for Read2-6mg.fq.gz Approx 95% complete for Read2-6mg.fq.gz Analysis complete for Read2-6mg.fq.gz Failed to process file Read2-6mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read2-6mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) Started analysis of Read2-7mg.fq.gz Approx 5% complete for Read2-7mg.fq.gz Approx 10% complete for Read2-7mg.fq.gz Approx 15% complete for Read2-7mg.fq.gz Approx 20% complete for Read2-7mg.fq.gz Approx 25% complete for Read2-7mg.fq.gz Approx 30% complete for Read2-7mg.fq.gz Approx 35% complete for Read2-7mg.fq.gz Approx 40% complete for Read2-7mg.fq.gz Approx 45% complete for Read2-7mg.fq.gz Approx 50% complete for Read2-7mg.fq.gz Approx 55% complete for Read2-7mg.fq.gz Approx 60% complete for Read2-7mg.fq.gz Approx 65% complete for Read2-7mg.fq.gz Approx 70% complete for Read2-7mg.fq.gz Approx 75% complete for Read2-7mg.fq.gz Approx 80% complete for Read2-7mg.fq.gz Approx 85% complete for Read2-7mg.fq.gz Approx 90% complete for Read2-7mg.fq.gz Approx 95% complete for Read2-7mg.fq.gz Analysis complete for Read2-7mg.fq.gz Failed to process file Read2-7mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read2-7mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) Started analysis of Read2-8gm.fq.gz Approx 5% complete for Read2-8gm.fq.gz Approx 10% complete for Read2-8gm.fq.gz Approx 15% complete for Read2-8gm.fq.gz Approx 20% complete for Read2-8gm.fq.gz Approx 25% complete for Read2-8gm.fq.gz Approx 30% complete for Read2-8gm.fq.gz Approx 35% complete for Read2-8gm.fq.gz Approx 40% complete for Read2-8gm.fq.gz Approx 45% complete for Read2-8gm.fq.gz Approx 50% complete for Read2-8gm.fq.gz Approx 55% complete for Read2-8gm.fq.gz Approx 60% complete for Read2-8gm.fq.gz Approx 65% complete for Read2-8gm.fq.gz Approx 70% complete for Read2-8gm.fq.gz Approx 75% complete for Read2-8gm.fq.gz Approx 80% complete for Read2-8gm.fq.gz Approx 85% complete for Read2-8gm.fq.gz Approx 90% complete for Read2-8gm.fq.gz Approx 95% complete for Read2-8gm.fq.gz Analysis complete for Read2-8gm.fq.gz Failed to process file Read2-8gm.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read2-8gm_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) Started analysis of Read2-9mg.fq.gz Approx 5% complete for Read2-9mg.fq.gz Approx 10% complete for Read2-9mg.fq.gz Approx 15% complete for Read2-9mg.fq.gz Approx 20% complete for Read2-9mg.fq.gz Approx 25% complete for Read2-9mg.fq.gz Approx 30% complete for Read2-9mg.fq.gz Approx 35% complete for Read2-9mg.fq.gz Approx 40% complete for Read2-9mg.fq.gz Approx 45% complete for Read2-9mg.fq.gz Approx 50% complete for Read2-9mg.fq.gz Approx 55% complete for Read2-9mg.fq.gz Approx 60% complete for Read2-9mg.fq.gz Approx 65% complete for Read2-9mg.fq.gz Approx 70% complete for Read2-9mg.fq.gz Approx 75% complete for Read2-9mg.fq.gz Approx 80% complete for Read2-9mg.fq.gz Approx 85% complete for Read2-9mg.fq.gz Approx 90% complete for Read2-9mg.fq.gz Approx 95% complete for Read2-9mg.fq.gz Analysis complete for Read2-9mg.fq.gz Failed to process file Read2-9mg.fq.gz java.io.FileNotFoundException: /sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM/Read2-9mg_fastqc.zip (Permission denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.(FileOutputStream.java:237) at java.base/java.io.FileOutputStream.(FileOutputStream.java:187) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.(HTMLReportArchive.java:80) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123) at java.base/java.lang.Thread.run(Thread.java:829) [?2004h(base) gskoksharova@genedev2:/sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM$ (base) gskoksharova@genedev2:/sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM$ fastqc *.fq.gz-h [?2004l FastQC - A high throughput sequence QC analysis tool SYNOPSIS fastqc seqfile1 seqfile2 .. seqfileN fastqc [-o output dir] [--(no)extract] [-f fastq|bam|sam] [-c contaminant file] seqfile1 .. seqfileN DESCRIPTION FastQC reads a set of sequence files and produces from each one a quality control report consisting of a number of different modules, each one of which will help to identify a different potential type of problem in your data. If no files to process are specified on the command line then the program will start as an interactive graphical application. If files are provided on the command line then the program will run with no user interaction required. In this mode it is suitable for inclusion into a standardised analysis pipeline. The options for the program as as follows: -h --help Print this help file and exit -v --version Print the version of the program and exit -o --outdir Create all output files in the specified output directory. Please note that this directory must exist as the program will not create it. If this option is not set then the output file for each sequence file is created in the same directory as the sequence file which was processed. --casava Files come from raw casava output. Files in the same sample group (differing only by the group number) will be analysed as a set rather than individually. Sequences with the filter flag set in the header will be excluded from the analysis. Files must have the same names given to them by casava (including being gzipped and ending with .gz) otherwise they won't be grouped together correctly. --nano Files come from nanopore sequences and are in fast5 format. In this mode you can pass in directories to process and the program will take in all fast5 files within those directories and produce a single output file from the sequences found in all files. --nofilter If running with --casava then don't remove read flagged by casava as poor quality when performing the QC analysis. --extract If set then the zipped output file will be uncompressed in the same directory after it has been created. If --delete is also specified then the zip file will be removed after the contents are unzipped. -j --java Provides the full path to the java binary you want to use to launch fastqc. If not supplied then java is assumed to be in your path. --noextract Do not uncompress the output file after creating it. You should set this option if you do not wish to uncompress the output when running in non-interactive mode. --nogroup Disable grouping of bases for reads >50bp. All reports will show data for every base in the read. WARNING: Using this option will cause fastqc to crash and burn if you use it on really long reads, and your plots may end up a ridiculous size. You have been warned! --min_length Sets an artificial lower limit on the length of the sequence to be shown in the report. As long as you set this to a value greater or equal to your longest read length then this will be the sequence length used to create your read groups. This can be useful for making directly comaparable statistics from datasets with somewhat variable read lengths. --dup_length Sets a length to which the sequences will be truncated when defining them to be duplicates, affecting the duplication and overrepresented sequences plot. This can be useful if you have long reads with higher levels of miscalls, or contamination with adapter dimers containing UMI sequences. -f --format Bypasses the normal sequence file format detection and forces the program to use the specified format. Valid formats are bam,sam,bam_mapped,sam_mapped and fastq --memory Sets the base amount of memory, in Megabytes, used to process each file. Defaults to 512MB. You may need to increase this if you have a file with very long sequences in it. --svg Save the graphs in the report in SVG format. -t --threads Specifies the number of files which can be processed simultaneously. Each thread will be allocated 250MB of memory so you shouldn't run more threads than your available memory will cope with, and not more than 6 threads on a 32 bit machine -c Specifies a non-default file which contains the list of --contaminants contaminants to screen overrepresented sequences against. The file must contain sets of named contaminants in the form name[tab]sequence. Lines prefixed with a hash will be ignored. -a Specifies a non-default file which contains the list of --adapters adapter sequences which will be explicity searched against the library. The file must contain sets of named adapters in the form name[tab]sequence. Lines prefixed with a hash will be ignored. -l Specifies a non-default file which contains a set of criteria --limits which will be used to determine the warn/error limits for the various modules. This file can also be used to selectively remove some modules from the output all together. The format needs to mirror the default limits.txt file found in the Configuration folder. -k --kmers Specifies the length of Kmer to look for in the Kmer content module. Specified Kmer length must be between 2 and 10. Default length is 7 if not specified. -q --quiet Suppress all progress messages on stdout and only report errors. -d --dir Selects a directory to be used for temporary files written when generating report images. Defaults to system temp directory if not specified. BUGS Any bugs in fastqc should be reported either to simon.andrews@babraham.ac.uk or in www.bioinformatics.babraham.ac.uk/bugzilla/ [?2004h(base) gskoksharova@genedev2:/sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM$ fastqc --noextract --nogroup -o fastqc *.fastq.gz [?2004l Specified output directory 'fastqc' does not exist [?2004h(base) gskoksharova@genedev2:/sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM$ fastqc --noextract --nogroup -o fastqc *.fastq.gzh*.fq.gz-h-noextract --nogroup -o fastqc *.fastq.gzfastqc --noextract --nogroup -o fastqc *.fastq.gzz *.fastq.gz *.fastq.gz *.fastq.gz *.fastq.gz *.fastq.gz *.fastq.gz/sf/storage/gmo/hic/out/by_User/Galya/misc/misc *.fastq.gz [?2004l Skipping '*.fastq.gz' which didn't exist, or couldn't be read [?2004h(base) gskoksharova@genedev2:/sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM$ fastqc --noextract --nogroup -o /sf/storage/gmo/hic/out/by_User/Galya/misc/misc *.fastq.gzfastqc *.fastq.gzh*.fq.gz-h-noextract --nogroup -o fastqc 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Read2-9mg.fq.gz Approx 80% complete for Read2-9mg.fq.gz Approx 85% complete for Read2-9mg.fq.gz Approx 90% complete for Read2-9mg.fq.gz Approx 95% complete for Read2-9mg.fq.gz Analysis complete for Read2-9mg.fq.gz [?2004h(base) gskoksharova@genedev2:/sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM$ (base) gskoksharova@genedev2:/sf/storage/gmo/hic/out/_RawReads/2025-28-11-FTM$ cd /sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/PCGH1692 [?2004l [?2004h(base) gskoksharova@genedev2:/sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/PCGH1692$ bamCoverage -b reads.bam -o coverage.bwPCGH1692-Gen053-PCRfree-4X.hg38.final.bam -o coverage.bw MPCGH1692-Gen053-PCRfree-4X.hg38.finalcoverage.bw.coverage.bw [?2004l Command 'bamCoverage' not found, but can be installed with: apt install python3-deeptools Please ask your administrator. [?2004h(base) gskoksharova@genedev2:/sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/PCGH1692$ conda env list [?2004l # conda environments: # base * /home/gskoksharova/miniconda3 samtools /home/gskoksharova/miniconda3/envs/samtools tools /home/gskoksharova/miniconda3/envs/tools /home/nyt/anaconda3 [?2004h(base) gskoksharova@genedev2:/sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/PCGH1692$ conda activate tools [?2004l [?2004h(tools) gskoksharova@genedev2:/sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/PCGH1692$ conda activate toolsenv list bamCoverage -b PCGH1692-Gen053-PCRfree-4X.hg38.final.bam -o PCGH1692-Gen053-PCRfree-4X.hg38.final.coverage.bw [?2004l [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai bamFilesList: ['PCGH1692-Gen053-PCRfree-4X.hg38.final.bam'] binLength: 50 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 50 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai [W::hts_idx_load2] The index file is older than the data file: PCGH1692-Gen053-PCRfree-4X.hg38.final.bai ^Z [1]+ Stopped bamCoverage -b PCGH1692-Gen053-PCRfree-4X.hg38.final.bam -o PCGH1692-Gen053-PCRfree-4X.hg38.final.coverage.bw [?2004h(tools) gskoksharova@genedev2:/sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/PCGH1692$ samtools index PCGH1692-Gen053-PCRfree-4X.hg38.final.bam [?2004l [?2004h(tools) gskoksharova@genedev2:/sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/PCGH1692$ samtools index PCGH1692-Gen053-PCRfree-4X.hg38.final.bambamCoverage -b PCGH1692-Gen053-PCRfree-4X.hg38.final.bam -o PCGH1692-Gen053-PCRfree-4X.hg38.final.coverage.bw [?2004l bamFilesList: ['PCGH1692-Gen053-PCRfree-4X.hg38.final.bam'] binLength: 50 numberOfSamples: None blackListFileName: None skipZeroOverZero: False bed_and_bin: False genomeChunkSize: None defaultFragmentLength: read length numberOfProcessors: 1 verbose: False region: None bedFile: None minMappingQuality: None ignoreDuplicates: False chrsToSkip: [] stepSize: 50 center_read: False samFlag_include: None samFlag_exclude: None minFragmentLength: 0 maxFragmentLength: 0 zerosToNans: False smoothLength: None save_data: False out_file_for_raw_data: None maxPairedFragmentLength: 1000 [?2004h(tools) gskoksharova@genedev2:/sf/storage/gmo/hic/out/by_User/Galya/rnaseq_bams/PCGH1692$